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Publishing Language: Chinese

Screening Regulatory Genes Related to Wheat Grain Protein Accumulation Based on Transcriptome and WGCNA Analysis

LiYuan PAN1YongJun WANG1HaiJun LI1Fu HOU1Jing LI1LiLi LI1SuYang SUN1,2,3( )
Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai’an 223001, Jiangsu
Zhongshan Laboratory of Biological Breeding, Jiangsu Academy of Agricultural Sciences, Nanjing 210014
Jiangsu Provincial Collaborative Innovation Center of Modern Industrial Technology for Grain Crops, Yangzhou University, Yangzhou 225009, Jiangsu
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Abstract

【Objective】

Common wheat, as an important food crop, plays a crucial role in global food security. Identifying the gene regulatory networks involved in wheat grain protein synthesis and determining key candidate genes will provide theoretical support for quality breeding and improvement of wheat.

【Method】

The study used wheat grains at six developmental stages (5, 10, 15, 20, 25, and 30 days post-anthesis) as research materials to summarize the pattern of protein accumulation in wheat grains. Transcriptome data and grain protein content phenotypic data were analyzed using the WGCNA (Weighted Gene Co-expression Network Analysis) method to construct weighted gene co-expression networks and identify key hub transcription factor (TFs) genes.

【Result】

The accumulation of protein content in wheat grains showed a trend of initial decline followed by an increase, reaching its lowest value (12.16%) at 25 days post-anthesis, with significant differences in protein content between adjacent developmental stages. A total of 25 427 differentially expressed genes (DEGs) were identified between adjacent developmental stages. Cluster analysis divided these DEGs into five groups (A-E), with group B containing the highest number of DEGs (10 906). A total of 1 022 transcription factors (TFs) from 49 families were identified, with the NAC family containing the most TFs (107). WGCNA analysis identified five co-expression modules significantly associated with protein content. The turquoise module showed the highest positive correlation with protein content (r=0.80, P=1×10-4). By integrating differentially expressed genes and weighted gene co-expression networks, six positively regulated hub TFs from the MIKC-MADS, TCP, TALE, and CPP families were identified in two modules (turquoise and blue). Further correlation analysis between the protein content phenotype of Huaimai 48 and gene expression levels at different time points revealed that the expression levels of five hub TFs were significantly positively correlated with the protein content phenotype. Specifically, TraesCS5B03G0740100 and TraesCS7D03G0590500 showed specific high expression in spike and grain tissues.

【Conclusion】

The study identified important modules (turquoise and blue) related to wheat protein content accumulation, screened six hub TFs, and identified that the expression levels of two hub TFs are significantly positively correlated with protein content and are specifically highly expressed in spike and grain tissues. These genes can serve as candidate genes for regulating protein accumulation in wheat grains.

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Cite this article:
PAN L, WANG Y, LI H, et al. Screening Regulatory Genes Related to Wheat Grain Protein Accumulation Based on Transcriptome and WGCNA Analysis. Scientia Agricultura Sinica, 2025, 58(6): 1065-1082. https://doi.org/10.3864/j.issn.0578-1752.2025.06.003

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Received: 04 August 2024
Accepted: 20 September 2024
Published: 16 March 2025
© 2025 The Journal of Scientia Agricultura Sinica